| Variant ID: vg1105342898 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 5342898 |
| Reference Allele: C | Alternative Allele: G |
| Primary Allele: C | Secondary Allele: G |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.01, others allele: 0.00, population size: 286. )
GCGTGGAACTAAACACAGCCCTACTACAAATCCAAAAGTCTGCCCCTTCAAGCTACTTAGAGGGAGAAAAACACCAATGTTACCATCCTTTAGGTCTCAA[C/G]
CTTCTGAATAATCAAAATGGTGGTGCATCAAGCATCTTCATTGTCATCCTCATTTCCCTCTTCGTAAGAGTCTTCGTCTTCATCTTCATCATCATCGTCT
AGACGATGATGATGAAGATGAAGACGAAGACTCTTACGAAGAGGGAAATGAGGATGACAATGAAGATGCTTGATGCACCACCATTTTGATTATTCAGAAG[G/C]
TTGAGACCTAAAGGATGGTAACATTGGTGTTTTTCTCCCTCTAAGTAGCTTGAAGGGGCAGACTTTTGGATTTGTAGTAGGGCTGTGTTTAGTTCCACGC
| Populations | Population Size | Frequency of C(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 99.70% | 0.20% | 0.13% | 0.00% | NA |
| All Indica | 2759 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica III | 913 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 88.50% | 6.20% | 5.21% | 0.00% | NA |
| Intermediate | 90 | 96.70% | 2.20% | 1.11% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1105342898 | C -> G | LOC_Os11g09970.1 | 3_prime_UTR_variant ; 28.0bp to feature; MODIFIER | silent_mutation | Average:51.24; most accessible tissue: Zhenshan97 root, score: 68.289 | N | N | N | N |
| vg1105342898 | C -> G | LOC_Os11g09960.1 | upstream_gene_variant ; 2393.0bp to feature; MODIFIER | silent_mutation | Average:51.24; most accessible tissue: Zhenshan97 root, score: 68.289 | N | N | N | N |